Evaluate gene sets identified by SDAN
Wei Sun
2024-07-12
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 24.00 25.00 25.00 25.52 26.00 27.00## [1] 40## [1] 24 24 24 24 24 24 24 25 25 25 25 25 25 25 25 25 25 25 25 25 25 26 26 26 26
## [26] 26 26 26 26 26 26 27 27 27 27 27 27 27 27 27## [1] 1021Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"
## [1] "MARS"
## [1] "MARS1" "SLA2"
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"##
## FALSE TRUE
## 1120 139##
## FALSE TRUE <NA>
## 71 1049 139gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: ZNRD1 POLR1H
## 2: C2orf43 LDAH
## 3: FAM45A DENND10
## 4: MTERF MTERF1
## 5: NARG2 ICE2
## 6: C6orf203 MTRES1
## 7: HRSP12 RIDA
## 8: FOPNL CEP20
## 9: WARS WARS1
## 10: LINS LINS1
## 11: RRNAD1 METTL25B
## 12: FAM122B PABIR2
## 13: WDYHV1 NTAQ1
## 14: HIST1H2BD H2BC5
## 15: AGPAT6 GPAT4
## 16: C1orf123 CZIB
## 17: KIAA1841 SANBR
## 18: C2orf44 WDCP
## 19: TMEM155 SMIM43
## 20: C7orf55 FMC1-LUC7L2
## 21: C9orf89 CARD19
## 22: C11orf82 DDIAS
## 23: XRCC6BP1 ATP23
## 24: MARS MARS1
## 25: C19orf55 PROSER3
## 26: HIST1H2AE H2AC8
## 27: QARS EPRS1
## 28: APITD1 CENPS-CORT
## 29: CCDC101 SGF29
## 30: PDDC1 GATD1
## 31: EFCAB4A CRACR2B
## 32: EIF2S3L EIF2S3B
## 33: HIST1H2BC H2BC5
## 34: WRB GET1
## 35: TMEM194B NEMP2
## 36: HIST1H4C H4C3
## 37: HIST1H4J H4C11
## 38: ZNF720 KRBOX5
## 39: HIST1H2BH H2BC9
## 40: FAM49A CYRIA
## 41: TTC37 SKIC3
## 42: C1orf85 GLMP
## 43: C9orf114 SPOUT1
## 44: HIST2H2AA4 H2AC19
## 45: HIST2H2BF H2BC18
## 46: C10orf128 TMEM273
## 47: TCTEX1D2 DYNLT2B
## 48: C17orf89 NDUFAF8
## 49: PHBP3 PHB1P3
## 50: SEPT7P7 SEPTIN7P7
## 51: LINC00493 SMIM26
## 52: HIST1H2BN H2BC15
## 53: ATP5J2 ATP5MF
## 54: AKAP2 PALM2AKAP2
## 55: WDR65 CFAP57
## 56: SRP14-AS1 SRP14-DT
## 57: CTC-436P18.1 SMIM15-AS1
## 58: HIST1H3G H3C8
## 59: EFTUD1P1 EFL1P1
## 60: ATP5A1P3 ATP5F1AP3
## 61: CCDC109B MCUB
## 62: C1orf63 RSRP1
## 63: TMEM66 SARAF
## 64: PCNXL2 PCNX2
## 65: ACRC GCNA
## 66: AMICA1 JAML
## 67: PRMT10 PRMT9
## 68: FAM102A EEIG1
## 69: SELM SELENOM
## 70: NBPF16 NBPF15
## 71: RPL9P9 RPL9P8
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]
dim(gene_info)## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1
## 3: ICA1 ICA1 ICA1
## 4: NDUFAF7 NDUFAF7 NDUFAF7
## 5: ST7 ST7 ST7## t1
## 1 2
## 1255 2## sym_in_data sym_limma gene_symbol
## 1: HIST1H2BD H2BC5 H2BC5
## 2: HIST1H2BC H2BC5 H2BC5
## 3: RPL9P8 RPL9P8 RPL9P8
## 4: RPL9P9 RPL9P8 RPL9P8Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]] = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp" "immune"## reactome go_bp immune
## 1692 7647 5219Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
##
## $immune
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5 162 193 197 199 199 200 200 200 200 1992Conduct enrichment analysis
## [1] 1259 3## sym_in_data sym_limma gene_symbol
## 1: C1orf112 C1orf112 C1orf112
## 2: MAD1L1 MAD1L1 MAD1L1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol")
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=120)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MCEE" "RPS17" "RPL34" "RPS12"
## [5] "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "SGSM2" "RPS27A" "RPL32" "RPS3A"
## [13] "RPL7" "RPL30" "RPL9" "RPS14"
## [17] "RPL27A" "RPLP2" "RPS27" "RPS23"
## [21] "RPS26" "RPL41" "RPS18" "CTD-2031P19.4"
## [1] 2
## [1] "C1orf112" "TNFRSF9" "WDR13" "ID3"
## [5] "CCRL2" "YIPF2" "FIGNL1" "SLC2A8"
## [9] "SPPL2A" "IRF8" "CCDC51" "SLC39A13"
## [13] "KIR3DL1" "GTSF1" "ZBED2" "YIPF6"
## [17] "TNFRSF18" "KIR2DL4" "GM2A" "KIR2DS4"
## [21] "UBE2D3P2" "RP4-742C19.12" "DBNDD2" "RP11-511H9.4"
## [25] "PHLDB3" "ANKRD37"
## [1] 3
## [1] "LTBP4" "ARHGEF18" "GPN2" "FARP1" "PPP1R32"
## [6] "C7orf55" "TAF10" "KBTBD2" "ATPAF2" "SGMS1"
## [11] "RUFY2" "PCNXL2" "FAM117B" "FBXO32" "EPB41"
## [16] "ATXN7" "ZNF589" "POLR2J3" "YPEL2" "NELL2"
## [21] "TSC22D2" "GPRASP1" "PPP1R10" "RP11-514P8.6" "HCG4P5"
## [1] 4
## [1] "RNF10" "CNOT2" "C3orf14" "AHI1" "APTX" "LINS"
## [7] "PLIN2" "C2orf44" "GLB1" "RRM2" "PCGF5" "CNOT10"
## [13] "EIF4ENIF1" "IFRD1" "DDX3Y" "TNRC6C" "TNRC6B" "UAP1"
## [19] "YPEL5" "CNOT6L" "NR4A2" "BTG2" "PFKFB3" "PLK3"
## [1] 5
## [1] "RABGAP1" "ERGIC2" "GOSR2" "CPD" "NCOA7" "MYB"
## [7] "NARF" "MAP3K6" "LIMD1" "VPS37A" "AGPAT6" "C1orf123"
## [13] "WDR41" "ASB8" "HIST1H4C" "RAB12" "DKK3" "PPP2R5C"
## [19] "CLDND1" "ARRDC2" "LEF1" "SSH2" "C9orf72" "NPAT"
## [25] "RALGAPA1"
## [1] 6
## [1] "ICA1" "GCFC2" "GLT8D1" "MAN2B1" "GBP1" "SCPEP1" "SLC41A2"
## [8] "CLSTN3" "MFSD6" "SLAMF8" "USF1" "ALG8" "MTHFD2L" "GNGT2"
## [15] "ITGAM" "NINJ2" "METRNL" "TMEM107" "PRF1" "BTLA" "NCR3"
## [22] "TRGV3" "TREX1" "KIR3DL2" "KIR2DL3"
## [1] 7
## [1] "ZNRD1" "TIMM9" "POP4" "POLR2I" "GNPTAB" "FAHD2A" "EPAS1"
## [8] "GALE" "UXT" "TMEM241" "TIMM10" "FHOD1" "UCK2" "MPPE1"
## [15] "GALK2" "MED11" "LZTFL1" "POLR2H" "IL15" "CDCA7L" "POP5"
## [22] "TRIM68" "PPARA" "UCKL1" "SELM"
## [1] 8
## [1] "FAM50B" "FCRL6" "CEP57L1" "CALM2P3"
## [5] "RP11-773D16.1" "CTD-2521M24.9" "C1orf63" "ACRC"
## [9] "AMICA1" "CDC42EP3" "ZMAT1" "FILIP1L"
## [13] "RBKS" "CHD2" "LDOC1" "PLGLB1"
## [17] "RP11-91K8.4" "CTD-2328D6.1" "PSMD6-AS2" "MTND4P12"
## [21] "RP11-727F15.9" "QRSL1P3" "RP11-320M16.1" "RP11-335G20.7"
## [25] "RP11-51J9.5"
## [1] 9
## [1] "CDKL1" "PIM2" "TFDP2" "TTLL4"
## [5] "CASP1" "APH1B" "PSEN2" "TMEM134"
## [9] "ANKRD28" "TRAV24" "PSMA6P1" "RP11-122G18.7"
## [13] "RP1-182O16.1" "RNU2-63P" "PHBP3" "RAB1C"
## [17] "AC002331.1" "NDUFA9P1" "RP11-305L7.3" "LINC00426"
## [21] "RPL37P23" "RP11-402J6.3" "SNORD3A" "PLXND1"
## [25] "APBA2" "PLA2G4B"
## [1] 10
## [1] "ZNF419" "PUS7L" "NAALADL1" "RP11-23P13.6"
## [5] "ZNF93" "WDR53" "C2orf76" "ZNF28"
## [9] "RPSAP54" "AC098614.2" "XXbac-B562F10.11" "RP11-2F9.3"
## [13] "RP3-342P20.2" "RP11-567G24.1" "RP11-247I13.6" "AC115617.2"
## [17] "GAPDHP2" "CTD-2301A4.3" "RPL7AP31" "CTB-4E7.1"
## [21] "RP11-307P22.1" "TRAV30" "RP11-209D14.4" "CTB-31O20.3"
## [25] "RP11-686D22.10" "CTB-52I2.4" "TMEM9B-AS1"
## [1] 11
## [1] "SMG6" "MS4A6A" "C2orf43" "L3HYPDH"
## [5] "PGPEP1" "NPL" "IFI44L" "IFI44"
## [9] "TMEM138" "TRANK1" "EDARADD" "TRGV10"
## [13] "TRGV5" "TRBV4-2" "TRAV8-2" "TRGC2"
## [17] "ST13P19" "RPL19P21" "TRGV2" "AC092580.4"
## [21] "RP3-395M20.8" "RP11-33B1.1" "CCL3L3" "CTD-2022H16.3"
## [25] "RP11-345J4.6" "ATP5A1P3"
## [1] 12
## [1] "PLA2G15" "TRPT1" "CMAHP" "ZNF816"
## [5] "RP11-383G10.3" "AC144530.1" "PKMP1" "RP11-32B5.1"
## [9] "RP11-271C24.3" "STARD4-AS1" "MAK" "MAN1C1"
## [13] "ACVR2A" "NBPF14" "C1orf162" "PLAC8"
## [17] "LDLRAP1" "NBPF10" "TMEM150A" "CD248"
## [21] "TRABD2A" "NBPF16" "AC084018.1" "CTD-3092A11.1"
## [25] "RP11-632K20.7" "WHAMMP2"
## [1] 13
## [1] "CHI3L2" "CD200" "PDE6B" "KHDC1"
## [5] "MFSD9" "FUOM" "TNFAIP8L2" "EFCAB4A"
## [9] "ZNF678" "CPT1B" "TRBV9" "TRAV29DV5"
## [13] "RP11-64B16.2" "RP13-383K5.4" "TPI1P2" "RP11-782C8.1"
## [17] "BDH2P1" "SNRPEP4" "LINC00484" "BHLHE40-AS1"
## [21] "RP11-179A18.1" "AC005329.7" "SRP14-AS1" "RP11-81H14.2"
## [25] "KB-1507C5.2" "USP30-AS1" "AP000462.1"
## [1] 14
## [1] "MFAP3" "FAR2" "SH3BP2" "PTPN4" "MICALL1" "CAPN15"
## [7] "CRTAM" "CD86" "MTFR1L" "HRSP12" "DPH6" "FGFBP2"
## [13] "KSR1" "FADS1" "RNF207" "CTLA4" "FRS2" "LRRC28"
## [19] "ZNF80" "PAAF1" "CADM1" "HIST1H4J" "SCML1" "EPHA4"
## [25] "MPP7"
## [1] 15
## [1] "CENPQ" "DHRS12" "RASSF4" "PRR4" "CENPO"
## [6] "ARHGEF1" "PIK3IP1" "RGCC" "EGR1" "PMEPA1"
## [11] "FOSB" "JUND" "SLC38A2" "FAM102A" "JUNB"
## [16] "GOLGA8A" "TTC3" "RGPD6" "MIR4461" "MTND2P28"
## [21] "MTND1P23" "ATP1B3-AS1" "RP11-44N11.1" "SLC7A5P1" "KCNQ1OT1"
## [1] 16
## [1] "WIPI1" "DERL2" "IL4R" "ABHD11" "PTP4A1" "RCOR3" "IFIT2" "TEP1"
## [9] "RSAD2" "FADS2" "BCAS3" "MX1" "AMFR" "FBXO22" "GNG4" "BOLA1"
## [17] "IFIT1" "AGER" "DNASE1" "PVT1" "NEK1" "SIK1" "DHRS3" "SERHL2"
## [1] 17
## [1] "MAD1L1" "CDC27" "CDKN3" "SPTLC2" "ERCC2" "GTF2H3"
## [7] "SMC4" "CACYBP" "CDC20" "STMN1" "CCR2" "CKS2"
## [13] "NPHP4" "CCNB1" "CDK7" "PWP1" "PMAIP1" "CEP78"
## [19] "HIRIP3" "CCNB2" "MYO1E" "ANAPC10" "SESTD1" "C17orf89"
## [25] "TMEM63A"
## [1] 18
## [1] "PTPN18" "NT5C2" "GALK1" "GORASP1"
## [5] "STK25" "CD160" "DHDDS" "NPC2"
## [9] "STYXL1" "KATNBL1" "WARS" "TATDN1"
## [13] "MITD1" "AMDHD2" "CTSB" "GEM"
## [17] "C11orf82" "MEI1" "TBCA" "SMIM19"
## [21] "SPATA13" "PSMG1" "ARHGAP11B" "ANAPC10P1"
## [25] "RP11-638I2.10"
## [1] 19
## [1] "DYRK4" "EGR2" "DTD2" "PIGW"
## [5] "CCDC30" "AC018804.7" "LDHBP2" "MYL5"
## [9] "AC012318.3" "RP11-350G8.3" "GK3P" "SKP1P1"
## [13] "AC093391.2" "RPS27AP2" "CTC-338M12.4" "PTGES3P1"
## [17] "AP000476.1" "AC018462.3" "EEF1A1P10" "HNRNPA1P16"
## [21] "MIR3661" "RP11-282O18.6" "RIMKLB" "RP1-187B23.1"
## [25] "RP13-488H8.1" "LINC00944" "RP11-1000B6.3"
## [1] 20
## [1] "TM7SF3" "GMPR2" "DUS4L" "LOXL3"
## [5] "FANCL" "RNF121" "TBCD" "GEMIN6"
## [9] "CETN3" "NDUFAF6" "PAQR4" "XRCC6BP1"
## [13] "RHEBL1" "NT5DC1" "LRTOMT" "TRAV13-1"
## [17] "NCKIPSD" "RP4-694B14.5" "RPF2P1" "GAPDHP73"
## [21] "RPL13P5" "CTC-436P18.1" "PAICSP4" "RP11-386G11.10"
## [25] "PMF1-BGLAP" "ACTBP9"
## [1] 21
## [1] "TBPL1" "NSMAF" "PMM1" "GZMB" "DDX49"
## [6] "BRD8" "HAVCR1" "MT2A" "NARG2" "PDZD2"
## [11] "GTF2A2" "DRAM2" "GSTM4" "CAPN12" "COA3"
## [16] "CMC1" "ZNF765" "CCL3L1" "TRAV14DV4" "LINC00493"
## [21] "AC104820.2" "RN7SL749P" "TPM3P6" "AC004069.2" "AL358333.1"
## [1] 22
## [1] "OCEL1" "FAM45A" "NME6" "ZNF613"
## [5] "LCORL" "EIF2S3L" "ABHD16B" "RPSAP47"
## [9] "TMEM194B" "METTL6" "RP11-12M9.4" "CD27-AS1"
## [13] "UBXN2B" "ACTBP8" "AC009506.2" "AC010878.3"
## [17] "CCT8P1" "PGAM4" "RP4-800M22.1" "SEPT7P7"
## [21] "PA2G4P4" "PA2G4P2" "RP11-446E9.1" "RP11-473N11.2"
## [25] "RP11-317N8.4" "RP11-493L12.6" "RP11-265N6.3"
## [1] 23
## [1] "FAH" "RRNAD1" "TMSB15B" "KIAA1841"
## [5] "LRRC45" "SNHG11" "AC004840.9" "NAP1L4P1"
## [9] "GEN1" "ZNF257" "TRAV16" "RP1-102E24.1"
## [13] "ATF4P3" "AC090804.1" "ZNF826P" "FAM21FP"
## [17] "RP11-394D2.1" "RNF138P1" "MIR146A" "SLC2A3P4"
## [21] "SF3A3P2" "RP11-416A17.6" "RP11-304L19.5" "RP11-1094M14.7"
## [25] "CTD-2545M3.2" "RP11-705C15.5"
## [1] 24
## [1] "ZNF268" "MDGA1" "MTERF" "CX3CR1"
## [5] "ADCK5" "THAP2" "ZNF683" "SLC9A9"
## [9] "CATSPER2P1" "TRAV19" "TRAV35" "KANSL1-AS1"
## [13] "RPS19P1" "RPL19P12" "RP11-119F19.2" "HNRNPKP2"
## [17] "BTF3P10" "ADH5P4" "AC007041.2" "RPS19P3"
## [21] "GAPDHP60" "RP11-613F22.5" "MIR3615" "LUZP6"
## [25] "RP11-297D21.4" "AC006129.4" "LINC00674"
## [1] 25
## [1] "IL18RAP" "TNFSF10" "PTGER2" "MTHFS"
## [5] "ASNSD1" "XCL1" "XCL2" "C9orf89"
## [9] "ZBTB39" "MT1E" "ENTPD5" "MT1X"
## [13] "ZNF720" "C10orf128" "TRBV20-1" "RSC1A1"
## [17] "NPM1P34" "RP11-262H14.3" "RP11-693N9.2" "ETF1P2"
## [21] "HSPA8P4" "HNRNPA1P55" "TRGV7" "TRAV1-2"
## [25] "EFTUD1P1" "HMGB1P8" "CTD-3214H19.4"
## [1] 26
## [1] "TIPIN" "DUSP12" "DEPDC5" "NSMCE4A"
## [5] "RAD51C" "AKR1A1" "TXNDC17" "TROAP"
## [9] "MMS22L" "SFR1" "PRIMPOL" "UBE2C"
## [13] "SWI5" "ZBTB8OS" "TYMS" "POLE"
## [17] "HIST1H2BC" "HIST2H2AA4" "STK19" "MDP1"
## [21] "RP11-365H23.1" "PIN4P1" "PPIL3" "HIST1H3G"
## [1] 27
## [1] "REXO1" "RP3-324O17.4" "ZNF684" "SLC35A5"
## [5] "TMEM19" "C19orf55" "MTHFD2P7" "PLA2G6"
## [9] "TRAV12-2" "TRDV1" "TRDC" "PDCL3P5"
## [13] "RP5-1053E7.3" "UBA52P6" "LYPLA1P3" "ARPC3P1"
## [17] "RP11-350G13.1" "TCP1P1" "PRDX3P1" "RP11-288E14.2"
## [21] "MAPKAPK5-AS1" "FAM200B" "RNU1-125P" "RP11-382J24.2"
## [25] "AC006483.1" "AC139149.1" "RP4-739H11.4"
## [1] 28
## [1] "MAP3K13" "OAS1" "ZNF85" "IL10"
## [5] "TMEM155" "TECPR1" "RP11-247I13.3" "TSTD1"
## [9] "PTGES3P2" "PATL2" "PET100" "GYG1P3"
## [13] "CNOT7P1" "CDC42P1" "Z97634.3" "ZEB1-AS1"
## [17] "GAPDHP38" "RBBP4P1" "RP11-889L3.4" "AP000620.1"
## [21] "RBBP4P5" "RP11-1012A1.7" "TPMTP1" "AC024592.12"
## [25] "TCEAL3" "AP001468.1"
## [1] 29
## [1] "CD84" "PON2" "KLRB1" "CCL4" "ACTR10" "KLRC1"
## [7] "BORA" "GCHFR" "CXCL13" "PANK4" "FCRL3" "MGAT4B"
## [13] "LGALS9C" "SLC38A9" "WRB" "HLA-DQA1" "CCL4L2" "FAM49A"
## [19] "SH2D1B" "MSH5" "CCL4L1" "KLRC2" "TCTEX1D2" "SAPCD1"
## [25] "MS4A1"
## [1] 30
## [1] "AGA" "GBA2" "RNF13" "USP48" "RABGGTA" "GABPB1" "GSR"
## [8] "ILVBL" "PPFIA1" "PPCDC" "PPOX" "TAMM41" "SEC24D" "FCGR3B"
## [15] "RNF25" "COG5" "ZNF232" "NFU1" "ETFDH" "MZT2A" "TDRD7"
## [22] "FCGR3A" "NR1D2" "WHAMMP3"
## [1] 31
## [1] "MBNL3" "AAAS" "SLC25A14" "LIN7B" "C17orf75" "COQ3"
## [7] "PRMT7" "FOPNL" "TPGS2" "COPS3" "LPP" "CXXC1"
## [13] "NTAN1" "CTDNEP1" "DALRD3" "ZNF511" "C1orf85" "TMSB4X"
## [19] "ATP5J2" "ABHD14A" "MIR142" "GGT7" "OBSCN" "MUC20"
## [25] "MALAT1"
## [1] 32
## [1] "STAU2" "NOP16" "YBX3" "NTHL1" "DOT1L" "DHX58"
## [7] "SLC11A2" "DKC1" "IMP4" "SCRN2" "PELP1" "UTP23"
## [13] "OXSM" "FAM122B" "DBF4B" "ZFP62" "ZNF431" "ZNF770"
## [19] "C9orf114" "ZBTB48" "POTEG" "MIR29B1" "RPS11P5" "AKAP2"
## [1] 33
## [1] "WDR7" "EMG1" "DEF8" "SPON2"
## [5] "HIST2H2BF" "RPS12P26" "GOT2P3" "RP4-728D4.2"
## [9] "CTB-33G10.1" "RASGRF2" "AOAH" "FRMD4A"
## [13] "CXCR5" "AC018720.10" "FAM169A" "HLA-J"
## [17] "RPS26P6" "RPS3AP26" "RP11-572P18.1" "RPL10P3"
## [21] "RPL9P8" "RPL3P4" "RPS3AP6" "HLA-W"
## [25] "RPL9P9" "RPL9P7"
## [1] 34
## [1] "CCL3" "POLD3" "P2RX5" "KIF4A" "ENO3" "NR2C1" "METTL8"
## [8] "DNPEP" "SLC12A4" "SAT1" "SNX14" "PRSS23" "TOMM40L" "TMPRSS3"
## [15] "B2M" "LAIR2" "DNAJC18" "METTL18" "AFMID" "CRYGS" "RGPD5"
## [22] "STK17B" "TMEM66" "EIF1" "CD55"
## [1] 35
## [1] "NHP2P1" "MCM9" "PECR" "NUDT7"
## [5] "CCDC28B" "IFI27" "ZNF749" "EEF1GP1"
## [9] "ZNF649" "ZNF525" "NPM1P32" "NPM1P33"
## [13] "AC009403.2" "RP11-378G13.2" "NPM1P19" "RP11-270C12.3"
## [17] "HNRNPA1P21" "RP11-809F4.2" "TSEN15P1" "RN7SL56P"
## [21] "RP11-552M11.4" "GMPSP1" "RP11-844P9.3" "HMGB1P24"
## [25] "RPPH1" "RP11-265N6.2" "RP13-638C3.4"
## [1] 36
## [1] "EVC" "NFE2L1" "UBXN8" "ZNF544" "RASGRP2"
## [6] "MGAT4A" "TXK" "TCF7" "SLC38A1" "BACH2"
## [11] "HECA" "NR4A3" "CCR7" "PLXDC1" "TIPARP"
## [16] "PRMT10" "DNHD1" "ZBTB20" "TSHZ2" "KLHL25"
## [21] "DENND5A" "SELL" "AC021593.1" "LTB" "RP11-285F7.2"
## [26] "ZNF10" "RP11-747H7.3"
## [1] 37
## [1] "VPS41" "POLA2" "USP28" "WDR3" "PIK3C3" "ULK2"
## [7] "KHSRP" "DHPS" "THOC5" "SNX8" "NUP85" "UROD"
## [13] "C19orf47" "WDR43" "BAP1" "NAA15" "MARS" "ATG13"
## [19] "DUSP28" "PIK3R4" "CHAMP1" "MBD5" "IFRD2" "NAA16"
## [1] 38
## [1] "ORMDL2" "TRAV21" "NAP1L1P3" "RP3-340B19.5"
## [5] "GS1-124K5.2" "EEF1A1P14" "RP11-254B13.4" "RPSAP4"
## [9] "MTRNR2L3" "HSPA8P5" "HNRNPA1P50" "ANP32AP1"
## [13] "AL161784.1" "CPQ" "FOXP1" "RCAN3"
## [17] "BTG1" "TC2N" "GPR183" "SATB1"
## [21] "POU6F1" "ACTBP12" "CHRM3-AS2" "CTD-2017D11.1"
## [25] "RP1-313I6.12" "RP11-434H6.7"
## [1] 39
## [1] "NDUFAF7" "ACADVL" "MTIF2" "MRPS33" "NDUFAF5" "CDK5RAP1"
## [7] "EARS2" "MTFMT" "SARS2" "GTPBP10" "THG1L" "ATPAF1"
## [13] "C6orf203" "MTO1" "MRRF" "GLUD1" "MALSU1" "MRPL55"
## [19] "NDUFS4" "METTL17" "MRPL48" "ZNF782" "MRPL23" "MRPL33"
## [25] "CCDC109B"
## [1] 40
## [1] "BCL3" "GTSE1" "RGS1" "CCDC77" "SMUG1"
## [6] "IFI6" "GLUL" "BRIP1" "IRF4" "PHAX"
## [11] "HOPX" "CXCR6" "PDDC1" "EFCAB7" "RNU2-2P"
## [16] "MIR155HG" "AC011747.4" "DGKA" "SKIL" "RASGEF1B"
## [21] "NPIPB3" "PER1" "NPIPB4" "KLRK1" "NPIPB5"
## [26] "MTATP6P1"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_1"
## [1] "MCEE" "RPS17" "RPL34" "RPS12"
## [5] "RPS25" "RPL21" "RPL5" "RPS10"
## [9] "SGSM2" "RPS27A" "RPL32" "RPS3A"
## [13] "RPL7" "RPL30" "RPL9" "RPS14"
## [17] "RPL27A" "RPLP2" "RPS27" "RPS23"
## [21] "RPS26" "RPL41" "RPS18" "CTD-2031P19.4"
## $reactome
## category
## 21 activation of the mrna upon binding of the cap binding complex and eifs and subsequent binding to 43s
## 117 cellular response to starvation
## 255 eukaryotic translation elongation
## 256 eukaryotic translation initiation
## 387 influenza infection
## 471 metabolism of amino acids and derivatives
## 547 nonsense mediated decay nmd
## 691 regulation of expression of slits and robos
## 734 response of eif2ak4 gcn2 to amino acid deficiency
## 783 rrna processing
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 21 0 1 11 15 0
## 117 0 1 21 33 0
## 255 0 1 21 31 0
## 256 0 1 21 30 0
## 387 0 1 21 37 0
## 471 0 1 21 42 0
## 547 0 1 21 31 0
## 691 0 1 21 31 0
## 734 0 1 21 30 0
## 783 0 1 21 40 0
##
## $go_bp
## category over_represented_pvalue
## 515 cytoplasmic translation 0.000000e+00
## 3691 ribosomal small subunit biogenesis 1.519549e-07
## 3693 ribosome biogenesis 3.069868e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 515 1 21 33 0.0000000000
## 3691 1 7 16 0.0003105198
## 3693 1 9 35 0.0004182183
##
## $immune
## category
## 54 gaucher pbmc yf vax stamaril unknown age 7dy dn
## 1944 gse22886 naive bcell vs neutrophil up
## 1974 gse22886 naive tcell vs dc up
## 2104 gse2405 0h vs 24h a phagocytophilum stim neutrophil up
## 2109 gse2405 0h vs 9h a phagocytophilum stim neutrophil dn
## 3108 gse34205 healthy vs flu inf infant pbmc up
## 4014 gse41978 id2 ko vs id2 ko and bim ko klrg1 low effector cd8 tcell dn
## 4016 gse41978 klrg1 high vs low effector cd8 tcell dn
## 1725 gse21670 untreated vs tgfb il6 treated cd4 tcell dn
## 1628 gse2124 ctrl vs lymphotoxin beta treated mln up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 54 0.000000e+00 1 12 32
## 1944 0.000000e+00 1 12 25
## 1974 0.000000e+00 1 12 33
## 2104 0.000000e+00 1 16 40
## 2109 0.000000e+00 1 15 37
## 3108 0.000000e+00 1 11 25
## 4014 0.000000e+00 1 11 32
## 4016 0.000000e+00 1 12 30
## 1725 5.565068e-12 1 9 17
## 1628 3.572682e-11 1 9 19
## FDR
## 54 0.00000e+00
## 1944 0.00000e+00
## 1974 0.00000e+00
## 2104 0.00000e+00
## 2109 0.00000e+00
## 3108 0.00000e+00
## 4014 0.00000e+00
## 4016 0.00000e+00
## 1725 3.15292e-09
## 1628 1.82171e-08
##
## [1] "set_4"
## [1] "RNF10" "CNOT2" "C3orf14" "AHI1" "APTX" "LINS"
## [7] "PLIN2" "C2orf44" "GLB1" "RRM2" "PCGF5" "CNOT10"
## [13] "EIF4ENIF1" "IFRD1" "DDX3Y" "TNRC6C" "TNRC6B" "UAP1"
## [19] "YPEL5" "CNOT6L" "NR4A2" "BTG2" "PFKFB3" "PLK3"
## $reactome
## category
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 954 tp53 regulates transcription of cell cycle genes
## 981 transcriptional regulation by tp53
## 172 deadenylation of mrna
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 952 5.539692e-08 1.0000000 5 6
## 954 4.270671e-07 1.0000000 5 8
## 981 2.121919e-05 0.9999986 7 35
## 172 9.227516e-05 0.9999994 3 4
## FDR
## 952 5.661566e-05
## 954 2.182313e-04
## 981 7.228670e-03
## 172 2.357630e-02
##
## $go_bp
## category
## 1917 nuclear transcribed mrna poly a tail shortening
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 3702 rna destabilization
## 2380 positive regulation of mrna metabolic process
## 1912 nuclear transcribed mrna catabolic process
## 3201 regulation of mrna catabolic process
## 3202 regulation of mrna metabolic process
## 2179 positive regulation of cellular catabolic process
## 1372 mrna catabolic process
## 3257 regulation of nuclear transcribed mrna poly a tail shortening
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917 3.257384e-11 1.0000000 7 8
## 1913 5.964863e-10 1.0000000 7 10
## 3702 1.204871e-08 1.0000000 7 14
## 2380 4.382508e-08 1.0000000 7 16
## 1912 4.542493e-08 1.0000000 7 15
## 3201 8.928398e-08 1.0000000 7 17
## 3202 4.629271e-07 1.0000000 7 21
## 2179 1.890462e-06 0.9999999 8 33
## 1372 2.026659e-06 0.9999999 7 24
## 3257 2.845476e-06 1.0000000 4 5
## FDR
## 1917 1.331293e-07
## 1913 1.218920e-06
## 3702 1.641435e-05
## 2380 3.713034e-05
## 1912 3.713034e-05
## 3201 6.081727e-05
## 3202 2.702833e-04
## 2179 9.203284e-04
## 1372 9.203284e-04
## 3257 1.162946e-03
##
## [1] "set_9"
## [1] "CDKL1" "PIM2" "TFDP2" "TTLL4"
## [5] "CASP1" "APH1B" "PSEN2" "TMEM134"
## [9] "ANKRD28" "TRAV24" "PSMA6P1" "RP11-122G18.7"
## [13] "RP1-182O16.1" "RNU2-63P" "PHBP3" "RAB1C"
## [17] "AC002331.1" "NDUFA9P1" "RP11-305L7.3" "LINC00426"
## [21] "RPL37P23" "RP11-402J6.3" "SNORD3A" "PLXND1"
## [25] "APBA2" "PLA2G4B"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 858 signaling by notch3 2.616135e-05 0.9999999
## numDEInCat numInCat FDR
## 858 3 5 0.02673689
##
## [1] "set_15"
## [1] "CENPQ" "DHRS12" "RASSF4" "PRR4" "CENPO"
## [6] "ARHGEF1" "PIK3IP1" "RGCC" "EGR1" "PMEPA1"
## [11] "FOSB" "JUND" "SLC38A2" "FAM102A" "JUNB"
## [16] "GOLGA8A" "TTC3" "RGPD6" "MIR4461" "MTND2P28"
## [21] "MTND1P23" "ATP1B3-AS1" "RP11-44N11.1" "SLC7A5P1" "KCNQ1OT1"
## $reactome
## category
## 544 ngf stimulated transcription
## 564 nuclear events kinase and transcription factor activation
## 862 signaling by ntrks
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 544 8.510968e-06 0.9999999 4 7
## 564 1.210001e-05 0.9999999 4 8
## 862 3.174730e-05 0.9999994 4 10
## FDR
## 544 0.006183104
## 564 0.006183104
## 862 0.010815248
##
## [1] "set_17"
## [1] "MAD1L1" "CDC27" "CDKN3" "SPTLC2" "ERCC2" "GTF2H3"
## [7] "SMC4" "CACYBP" "CDC20" "STMN1" "CCR2" "CKS2"
## [13] "NPHP4" "CCNB1" "CDK7" "PWP1" "PMAIP1" "CEP78"
## [19] "HIRIP3" "CCNB2" "MYO1E" "ANAPC10" "SESTD1" "C17orf89"
## [25] "TMEM63A"
## $reactome
## category
## 456 m phase
## 50 apc c cdc20 mediated degradation of cyclin b
## 138 condensation of prometaphase chromosomes
## 500 mitotic metaphase and anaphase
## 501 mitotic prometaphase
## 390 inhibition of the proteolytic activity of apc c required for the onset of anaphase by mitotic spindle checkpoint compone
## 52 apc c mediated degradation of cell cycle proteins
## 283 formation of rna pol ii elongation complex
## 286 formation of the early elongation complex
## 370 hiv transcription elongation
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 456 7.030593e-06 0.9999995 8 43
## 50 1.690017e-05 0.9999998 4 7
## 138 2.101969e-05 1.0000000 3 3
## 500 2.392556e-05 0.9999988 6 24
## 501 3.095286e-05 0.9999983 6 25
## 390 8.254878e-05 0.9999995 3 4
## 52 9.599288e-05 0.9999973 4 10
## 283 2.026152e-04 0.9999975 3 5
## 286 2.026152e-04 0.9999975 3 5
## 370 2.026152e-04 0.9999975 3 5
## FDR
## 456 0.006112982
## 50 0.006112982
## 138 0.006112982
## 500 0.006112982
## 501 0.006326766
## 390 0.012942095
## 52 0.012942095
## 283 0.012942095
## 286 0.012942095
## 370 0.012942095
##
## $go_bp
## category over_represented_pvalue
## 1318 mitotic cell cycle phase transition 6.079680e-07
## 1221 meiotic cell cycle 8.499976e-06
## 2926 regulation of chromosome segregation 2.116535e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1318 1.0000000 9 42 0.002484765
## 1221 0.9999996 6 20 0.017369700
## 2926 0.9999993 5 14 0.028834257
##
## $immune
## category
## 3590 gse39556 cd8a dc vs nk cell mouse 3h post polyic inj up
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3590 2.650089e-06 0.9999999 7 28
## FDR
## 3590 0.0135128
##
## [1] "set_26"
## [1] "TIPIN" "DUSP12" "DEPDC5" "NSMCE4A"
## [5] "RAD51C" "AKR1A1" "TXNDC17" "TROAP"
## [9] "MMS22L" "SFR1" "PRIMPOL" "UBE2C"
## [13] "SWI5" "ZBTB8OS" "TYMS" "POLE"
## [17] "HIST1H2BC" "HIST2H2AA4" "STK19" "MDP1"
## [21] "RP11-365H23.1" "PIN4P1" "PPIL3" "HIST1H3G"
## $reactome
## category over_represented_pvalue
## 212 dna replication pre initiation 2.649729e-05
## 211 dna replication 5.670078e-05
## 468 meiotic recombination 1.045790e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 212 0.9999991 5 19 0.02708024
## 211 0.9999976 5 22 0.02897410
## 468 0.9999969 4 13 0.03562659
##
## [1] "set_36"
## [1] "EVC" "NFE2L1" "UBXN8" "ZNF544" "RASGRP2"
## [6] "MGAT4A" "TXK" "TCF7" "SLC38A1" "BACH2"
## [11] "HECA" "NR4A3" "CCR7" "PLXDC1" "TIPARP"
## [16] "PRMT10" "DNHD1" "ZBTB20" "TSHZ2" "KLHL25"
## [21] "DENND5A" "SELL" "AC021593.1" "LTB" "RP11-285F7.2"
## [26] "ZNF10" "RP11-747H7.3"
## $immune
## category
## 1268 gse17974 ctrl vs act il4 and anti il12 24h cd4 tcell up
## 56 goldrath eff vs memory cd8 tcell dn
## 136 gse11057 eff mem vs cent mem cd4 tcell dn
## 2958 gse32255 wt unstim vs jmjd2d knockdown 4h lps stim dc up
## 3608 gse3982 bcell vs cent memory cd4 tcell dn
## 2462 gse27241 wt vs rorgt ko th17 polarized cd4 tcell treated with digoxin dn
## 4597 gse7219 unstim vs lps and anti cd40 stim dc up
## 4599 gse7219 unstim vs lps and anti cd40 stim nik nfkb2 ko dc up
## 5060 scherer pbmc apsv wetvax age 18 32yo 5 to 7dy dn
## 425 gse13547 ctrl vs anti igm stim zfx ko bcell 12h dn
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1268 3.933068e-06 0.9999998 6 20
## 56 4.934628e-06 0.9999998 6 23
## 136 7.856450e-06 0.9999997 6 20
## 2958 1.125513e-05 0.9999995 6 22
## 3608 1.420646e-05 0.9999995 5 15
## 2462 2.907447e-05 0.9999989 5 16
## 4597 3.278495e-05 0.9999980 6 28
## 4599 4.373084e-05 0.9999972 6 29
## 5060 4.633864e-05 0.9999969 6 31
## 425 4.748952e-05 0.9999978 5 19
## FDR
## 1268 0.01258083
## 56 0.01258083
## 136 0.01335335
## 2958 0.01434748
## 3608 0.01448775
## 2462 0.02388150
## 4597 0.02388150
## 4599 0.02421491
## 5060 0.02421491
## 425 0.02421491
##
## [1] "set_38"
## [1] "ORMDL2" "TRAV21" "NAP1L1P3" "RP3-340B19.5"
## [5] "GS1-124K5.2" "EEF1A1P14" "RP11-254B13.4" "RPSAP4"
## [9] "MTRNR2L3" "HSPA8P5" "HNRNPA1P50" "ANP32AP1"
## [13] "AL161784.1" "CPQ" "FOXP1" "RCAN3"
## [17] "BTG1" "TC2N" "GPR183" "SATB1"
## [21] "POU6F1" "ACTBP12" "CHRM3-AS2" "CTD-2017D11.1"
## [25] "RP1-313I6.12" "RP11-434H6.7"
## $immune
## category over_represented_pvalue
## 1580 gse20727 h2o2 vs ros inhibitor treated dc up 1.940795e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 1580 1 5 19 0.0009896112
##
## [1] "set_39"
## [1] "NDUFAF7" "ACADVL" "MTIF2" "MRPS33" "NDUFAF5" "CDK5RAP1"
## [7] "EARS2" "MTFMT" "SARS2" "GTPBP10" "THG1L" "ATPAF1"
## [13] "C6orf203" "MTO1" "MRRF" "GLUD1" "MALSU1" "MRPL55"
## [19] "NDUFS4" "METTL17" "MRPL48" "ZNF782" "MRPL23" "MRPL33"
## [25] "CCDC109B"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation 0.000000e+00 1
## 986 translation 1.281153e-07 1
## numDEInCat numInCat FDR
## 495 8 9 0.000000e+00
## 986 10 46 6.546692e-05
##
## $go_bp
## category over_represented_pvalue
## 1301 mitochondrial gene expression 0.000000e+00
## 1311 mitochondrial translation 0.000000e+00
## 1307 mitochondrial rna metabolic process 3.346653e-07
## 3989 trna metabolic process 2.827013e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1301 1.0000000 12 16 0.0000000000
## 1311 1.0000000 10 13 0.0000000000
## 1307 1.0000000 5 7 0.0004559257
## 3989 0.9999984 6 23 0.0288850024
##
## [1] "set_40"
## [1] "BCL3" "GTSE1" "RGS1" "CCDC77" "SMUG1"
## [6] "IFI6" "GLUL" "BRIP1" "IRF4" "PHAX"
## [11] "HOPX" "CXCR6" "PDDC1" "EFCAB7" "RNU2-2P"
## [16] "MIR155HG" "AC011747.4" "DGKA" "SKIL" "RASGEF1B"
## [21] "NPIPB3" "PER1" "NPIPB4" "KLRK1" "NPIPB5"
## [26] "MTATP6P1"
## $immune
## category over_represented_pvalue
## 1806 gse22103 unstim vs lps stim neutrophil up 2.107416e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 1806 1 5 12 0.01074572Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8958527 478.5 17165476 916.8 NA 17165476 916.8
## Vcells 19141219 146.1 57216267 436.6 65536 78485130 598.8## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
## [2] GenomicFeatures_1.50.4
## [3] GenomicRanges_1.50.2
## [4] GenomeInfoDb_1.34.9
## [5] org.Hs.eg.db_3.16.0
## [6] AnnotationDbi_1.60.2
## [7] IRanges_2.32.0
## [8] S4Vectors_0.36.2
## [9] Biobase_2.58.0
## [10] BiocGenerics_0.44.0
## [11] goseq_1.50.0
## [12] geneLenDataBase_1.34.0
## [13] BiasedUrn_2.0.10
## [14] fgsea_1.24.0
## [15] biomaRt_2.54.1
## [16] limma_3.54.2
## [17] tidyr_1.3.0
## [18] ggpubr_0.6.0
## [19] ggplot2_3.4.2
## [20] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 tools_4.2.3
## [9] backports_1.4.1 bslib_0.4.2
## [11] utf8_1.2.3 R6_2.5.1
## [13] mgcv_1.8-42 DBI_1.1.3
## [15] colorspace_2.1-0 withr_2.5.0
## [17] tidyselect_1.2.0 prettyunits_1.1.1
## [19] bit_4.0.5 curl_5.0.1
## [21] compiler_4.2.3 cli_3.6.1
## [23] xml2_1.3.4 DelayedArray_0.24.0
## [25] rtracklayer_1.58.0 sass_0.4.5
## [27] scales_1.2.1 rappdirs_0.3.3
## [29] Rsamtools_2.14.0 stringr_1.5.0
## [31] digest_0.6.31 rmarkdown_2.21
## [33] XVector_0.38.0 pkgconfig_2.0.3
## [35] htmltools_0.5.5 MatrixGenerics_1.10.0
## [37] dbplyr_2.3.2 fastmap_1.1.1
## [39] rlang_1.1.0 rstudioapi_0.14
## [41] RSQLite_2.3.1 BiocIO_1.8.0
## [43] jquerylib_0.1.4 generics_0.1.3
## [45] jsonlite_1.8.4 BiocParallel_1.32.6
## [47] dplyr_1.1.2 car_3.1-2
## [49] RCurl_1.98-1.12 magrittr_2.0.3
## [51] GO.db_3.16.0 GenomeInfoDbData_1.2.9
## [53] Matrix_1.6-4 Rcpp_1.0.10
## [55] munsell_0.5.0 fansi_1.0.4
## [57] abind_1.4-5 lifecycle_1.0.3
## [59] stringi_1.7.12 yaml_2.3.7
## [61] carData_3.0-5 SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0 BiocFileCache_2.6.1
## [65] grid_4.2.3 blob_1.2.4
## [67] parallel_4.2.3 crayon_1.5.2
## [69] lattice_0.20-45 splines_4.2.3
## [71] Biostrings_2.66.0 cowplot_1.1.1
## [73] hms_1.1.3 KEGGREST_1.38.0
## [75] knitr_1.44 pillar_1.9.0
## [77] rjson_0.2.21 ggsignif_0.6.4
## [79] codetools_0.2-19 fastmatch_1.1-3
## [81] XML_3.99-0.14 glue_1.6.2
## [83] evaluate_0.20 png_0.1-8
## [85] vctrs_0.6.2 gtable_0.3.3
## [87] purrr_1.0.1 cachem_1.0.7
## [89] xfun_0.39 broom_1.0.4
## [91] restfulr_0.0.15 rstatix_0.7.2
## [93] tibble_3.2.1 GenomicAlignments_1.34.1
## [95] memoise_2.0.1